After being jailed for solving another mystery, the Mystery Inc. gang stumbles upon another mystery: a gruesome monster lurking underneath the town and cocooning everyone who comes near in green goop.

The gang finally follows the trail to find the hidden treasure, but they didn't think The Freak would go after them. On the other hand, many truths are revealed, including the goal of Professor Pericles and the true identity of Fred's parents. And as if that were not enough, the gang faces a big problem when the parents get angry due to the behavior of their sons. And just when the mystery of the town is at its highest level, does this mean the end of the gang or the beginning of a new problem?

Mystery Inc. has disbanded. Crystal Cove is attacked by a Man-Baby called Crybaby Clown. Mayor Nettles is approached by a mysterious figure who gives her the files on Mystery Inc. while stating that she has to get Mystery Inc. back together.

Fred tries to get Daphne back. Crybaby Clown returns to rob Crystal Cove and kidnaps Daphne as well. Daphne is rescued and agrees to return to the gang. Mr. E tries to re-recruit Angel Dynamite.